This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see netSmooth.
Bioconductor version: 3.9
netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.
Author: Jonathan Ronen [aut, cre], Altuna Akalin [aut]
Maintainer: Jonathan Ronen <yablee at gmail.com>
Citation (from within R,
enter citation("netSmooth")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("netSmooth")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("netSmooth")
HTML | R Script | Generation of PPI graph |
HTML | R Script | netSmooth example |
Reference Manual |
biocViews | Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
Version | 1.4.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (1.5 years) |
License | GPL-3 |
Depends | R (>= 3.5), scater(>= 1.9.20), clusterExperiment(>= 2.1.6) |
Imports | entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array |
LinkingTo | |
Suggests | knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel |
SystemRequirements | |
Enhances | |
URL | https://github.com/BIMSBbioinfo/netSmooth |
BugReports | https://github.com/BIMSBbioinfo/netSmooth/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | netSmooth_1.4.0.tar.gz |
Windows Binary | netSmooth_1.4.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | netSmooth_1.4.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/netSmooth |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/netSmooth |
Package Short Url | https://bioconductor.org/packages/netSmooth/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: